METAP2 RNA-Seq in HepG2

General Information


RBP	METAP2
Cell_Line	HepG2
Method	shRNA
Exp_Name	METAP2-BGHLV16-HepG2
ENCODE_series_ID	ENCSR593JUF
Batch_ID	BGHLV16
Pool ID	Pool-141001
Local_Set_Name	set16
ENCODE_KD_Exp_ID	ENCSR992JGE
ENCODE_CN_Exp_ID	ENCSR689PHN
Rep1	METAP2_BGHLV16_33
Rep2	METAP2_BGHLV16_34
CN1	NT_BGHLV16_1
CN2	NT_BGHLV16_2
Rep1_qPCR	66.8
Rep2_qPCR	76.2
Rep1_WB	92.3
Rep2_WB	92.0
Antibody Cat#	A303-419A
Antibody Lot#	A303-419A
Antibody DCC ID	ENCAB441VBJ
Status	Released
Project	ENCODE3
ID	420

Experiment Information (Status: Released)

	BGHLV16-33	BGHLV16-34
idx	201	202
TRCN#_or_BGC#	TRCN0000050581	TRCN0000050581
shRNA_or_gRNA_sequence	GCAGAAGCACATCGACAAGTT	GCAGAAGCACATCGACAAGTT
PAM
Name	METAP2	METAP2
Sample_ID	BGHLV16-33	BGHLV16-34
transduction_Date	7/31/2014	7/31/2014
days
RBP_name	METAP2	METAP2
qPCR_result	66.8	76.2
Ave_qPCR	71.5
RT-qPCR_primer-F	gcagaagcacatcgacaagt
RT-qPCR_primer-R	tgcgtgaacagtcttccaac
protein_conc	3084	3222
WB_result	92.3	92.0
Ave_WB	92.2
WB_DONE_date	3/27/2015
MW	53kdA
IP	1	1
antibody_Cat#	A303-419A	A303-419A
Antibody DCC ID	ENCAB441VBJ	ENCAB441VBJ
submitted_to_DCC_date	5/6/2015
Rep1_TPM	58.5	0
Rep2_TPM	46.8	0
Action
Library_start_date	9/23/2014	9/23/2014
repeat_library
Note
ID	2266	2267

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
METAP2	Product_ID: A303-419A Lot_ID: 1 Source: Bethyl Labs Target Name: METAP2-human

Experiment Status

	BGHLV16-33	BGHLV16-34
Sample_ID	BGHLV16-33	BGHLV16-34
Sample Name	METAP2_BGHLV16_33	METAP2_BGHLV16_34
Sample Name	METAP2_BGHLV16_33	METAP2_BGHLV16_34
RBP	METAP2	METAP2
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2014-12-11	2014-12-11
Project	ENCODE3	ENCODE3
Note
ID	564	565

Library-Prep
Sequencing

Library-Prep Information

	BGHLV16-33	BGHLV16-34
Sample #
Sample Name	METAP2-BGHLV16-33	METAP2-BGHLV16-34
Sample_Name_Alias	METAP2_BGHLV16_33	METAP2_BGHLV16_34
Index Well Position	S15	S16
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2014-09-23	2014-09-23
Lib_ID	Lib-140923	Lib-140923
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV16-17/set1/G7.png	DNA_Library_LV16-17/set1/H7.png
RIN	9.5	9.5
libSample_RNA_Well	RNA_Library_LV16-17-18/set1/E1.png	RNA_Library_LV16-17-18/set1/F1.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV16-33	BGHLV16-34
RBP	METAP2	METAP2
Batch_ID	BGHLV16	BGHLV16
WB_result	92.300	92.000
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2248	2249

Sequencing Information

	BGHLV16-33	BGHLV16-34	BGHLV16-34
Sample_ID	BGHLV16-33	BGHLV16-34	BGHLV16-34
Sample Name	METAP2_BGHLV16_33	METAP2_BGHLV16_34	METAP2_BGHLV16_34
Pool ID	Pool-141001	Pool-141001	Pool-151215B
LocalServer_folder	set16	set16	set16
total_reads	84,800,000	15,970,000	32,108,562
total_aligned_reads	76,711,114	9,994,982	23,741,562
unique_aligned_reads	72,382,066	9,425,418	22,369,306
percent_uniqueAligned	0.85356	0.59020	0.69668
correlation_replicates	0.988299	0.988299
spikein_reads	215,238	36,556	81,600
percent_spikeins	0.00254	0.00229	0.00254
original_ReadLength	100	100	100
QC_Status	Submitted	Submitted	Submitted
ID	890	891	1375

Data Submission Information

	BGHLV16-33	BGHLV16-33
ENCODE_alias	brenton-graveley:METAP2_BGHLV16	brenton-graveley:METAP2-BGHLV16-HepG2
ENCODE_accession	ENCSR992JGE	ENCSR593JUF
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV16-33	BGHLV16-33
Sample Name	METAP2_BGHLV16_33	METAP2_BGHLV16_33
Selected	Yes	Yes
Status	Released	Released
Status_Date	2014-12-08	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	2850	6810

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
METAP2_BGHLV16_33_ATGTCA_L007_R1_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	890	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14290
METAP2_BGHLV16_33_ATGTCA_L007_R2_001.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	890	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14316
METAP2_BGHLV16_33_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	890					GRCh38	V40	METAP2_BGHLV16_33_ATGTCA_L007_R1_001.fastq.gz,METAP2_BGHLV16_33_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	14342
METAP2_BGHLV16_33_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	890					GRCh38	V40	METAP2_BGHLV16_33/Aligned.sortedByCoord.out.bam		ENCORE2	14368
METAP2_BGHLV16_33_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	890					GRCh38	V40	METAP2_BGHLV16_33/Aligned.sortedByCoord.out.bam		ENCORE2	14394
METAP2_BGHLV16_33_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	890					GRCh38	V40	METAP2_BGHLV16_33/Aligned.sortedByCoord.out.bam		ENCORE2	14420
METAP2_BGHLV16_33_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	890					GRCh38	V40	METAP2_BGHLV16_33/Aligned.sortedByCoord.out.bam		ENCORE2	14446
METAP2_BGHLV16_33_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	890					GRCh38	V40	METAP2_BGHLV16_33_ATGTCA_L007_R1_001.fastq.gz,METAP2_BGHLV16_33_ATGTCA_L007_R2_001.fastq.gz		ENCORE2	14472
METAP2_BGHLV16_34_CCGTCC_L007_R1_001.merged.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	891	HiSeq2000	100	paired-ended	1				NT_BGHLV16_1_ATCACG_L005_R1_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R1_001.fastq.gz	ENCODE3	14291
METAP2_BGHLV16_34_CCGTCC_L007_R2_001.merged.fastq.gz	ENCODE_DATA/set16/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	891	HiSeq2000	100	paired-ended	2				NT_BGHLV16_1_ATCACG_L005_R2_001.fastq.gz,NT_BGHLV16_2_CGATGT_L005_R2_001.fastq.gz	ENCODE3	14317
METAP2_BGHLV16_34_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	891					GRCh38	V40	METAP2_BGHLV16_34_CCGTCC_L007_R1_001.merged.fastq.gz,METAP2_BGHLV16_34_CCGTCC_L007_R2_001.merged.fastq.gz		ENCORE2	14343
METAP2_BGHLV16_34_Signal.Unique.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	891					GRCh38	V40	METAP2_BGHLV16_34/Aligned.sortedByCoord.out.bam		ENCORE2	14369
METAP2_BGHLV16_34_Signal.Unique.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	891					GRCh38	V40	METAP2_BGHLV16_34/Aligned.sortedByCoord.out.bam		ENCORE2	14395
METAP2_BGHLV16_34_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	891					GRCh38	V40	METAP2_BGHLV16_34/Aligned.sortedByCoord.out.bam		ENCORE2	14421
METAP2_BGHLV16_34_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set16/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	891					GRCh38	V40	METAP2_BGHLV16_34/Aligned.sortedByCoord.out.bam		ENCORE2	14447
METAP2_BGHLV16_34_quant.sf	ENCODE_DATA/set16/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	891					GRCh38	V40	METAP2_BGHLV16_34_CCGTCC_L007_R1_001.merged.fastq.gz,METAP2_BGHLV16_34_CCGTCC_L007_R2_001.merged.fastq.gz		ENCORE2	14473